There are some thing that are contradictory to modern science. Like evolution(human) .
So if a person who interpret The Holy Quran(some verse) as a metaphor will he be committing kufr.
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Prophecy has ended with Muhammad (p.b.u.h) as childhood ends. All revelation has been adapted to the maturity of mankind. Like parents explain the world to their children, revelation was adapted to the knowledge of the people who received it. Natural science was not revealed. As we can not stay in the world how it has been explained to us in our childhood, we can not refuse knowledge that mankind has gained after the ages of prophecy. As a consequence, we have to look on the revelation from our point of view and think about what God wanted to tell the people of their time and what it means to us. God reveals to whom He wills and as much as He wills.